A short guide for molecular dynamics simulations of RNA systems.
As a result of important methodological advances and of the rapid growth of experimental data, the number of molecular dynamics (MD) simulations related to RNA systems has significantly increased. However, such MD simulations are not straightforward and great care has to be exerted during the setup stage in order to choose the appropriate MD package, force fields and ionic conditions. Furthermore, the choice and a correct evaluation of the main characteristics of the starting structure are primordial for the generation of informative and reliable MD trajectories since experimental structures are not void of inaccuracies and errors. The aim of this review is to provide, through numerous examples, practical guidelines for the setup of MD simulations, the choice of ionic conditions and the detection and correction of experimental inaccuracies in order to start MD simulations of nucleic acid systems under the best auspices.
Hashem
Yaser
Y
Architecture et Réactivité de l'ARN, Université Louis Pasteur de Strasbourg, IBMC, CNRS, 15 rue René Descartes, 67084 Strasbourg Cedex, France.
Auffinger
Pascal
P
D003198:Computer Simulation; D018360:Crystallography, X-Ray; D006859:Hydrogen / Q000737:chemistry; D007477:Ions / Q000737:chemistry; D008958:Models, Molecular; D012313:RNA / Q000737:chemistry*; D015203:Reproducibility of Results; D055672:Static Electricity; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D007477:Ions; D014867:Water; D012313:RNA; D006859:Hydrogen